Software

ADF MAGE-ML
Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML).
http://adfconverter.sourceforge.net/

AlmaKnowledgeServer
Text mining tool for genomics, proteomics platforms and drug discovery.
http://www.timelogic.com/aks/index.html

AnnHyb
Free software for working with and managing nucleotide sequences in multiple formats. Features include sequence annotation, restriction analysis, pattern searching, retrieval from servers. Released under GNU Public Licence.
http://bioinformatics.org/annhyb/

The ARB Project
A free sequence database application for Unix. It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and generation, genome annotation and visualization. In addition to the integrated user-interface the ARB database can be accessed using Perl or C.
http://www.arb-home.de

ARCiB -- Accessible Retired Computers in Biology
NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental support, especially in structual biology, for software packages on various platforms.
http://arcib.dowling.edu/

Biological Concept Diagram Editor
A tool designed for efficient knowledge and data capture from electronic resources for sharing, mining and presentation purposes.
http://arrayanalysis.mbni.med.umich.edu/draw/

Darwin
An interactive tool for peptide and nucleotide sequence analysis.
http://cbrg.inf.ethz.ch/Darwin/index.html

DNA Counter
Small free Windows program to calculate nucleotides frequencies in DNA sequences.
http://www.dnabaser.com/download/DNA-Counter/index.html

DNAMAN
Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X.
http://www.lynnon.com

DNPTrapper
A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
http://dnptrapper.sourceforge.net/

Expression Profiler
An open, extensible web-based collaborative platform for microarray gene expression, sequence and PPI data analysis, exposing distinct chainable components for clustering, pattern discovery, statistics, machine-learning algorithms and visualization.
http://www.ebi.ac.uk/expressionprofiler/

FASTA Converter
Free Windows tool for merging multiple FASTA files into a single FASTA file.
http://www.dnabaser.com/download/FASTA-Converter/index.html

Friend
An integrated multiple structure visualization and multiple sequence alignment application. Available for Windows, Linux.
http://mozart.bio.neu.edu/friend/friend.html

GDE
An integrated linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment (GDE). Contains binaries for Linux and Mac OS X, documentation, screenshots, references, and organism specific interfaces.
http://www.bioafrica.net/GDElinux/index.html

Genespotter
Commercial Windows software for analyzing biochip image data.
http://www.genespotter.de

Genome-tools Web Interface
Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format.
http://sourceforge.net/projects/genome-tools/

Gints
Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
http://gints.free.fr/english/eng_whatsAbout.htm

GoCore
GoCore is a free Excel based tool for protein sequence alignment, comparisons and functional predictions in a simple, visually appealing, manner.
http://www.helsinki.fi/project/ritvos/GoCore/

INCA - INteractive Codon Analysis
Windows software that computes and charts codon and amino acid frequencies in whole genomes. Produces fully customizable scatter plots with the possibility to export graphics or text files for further analysis. Free for academic users.
http://www.bioinfo-hr.org/inca

JAligner
Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
http://jaligner.sourceforge.net/

JSTRING
Java program for searching Tandem Repeats (TR) in a DNA sequence. It shows the results also in a graphical format.
http://bioinf.dms.med.uniroma1.it/JSTRING/

KoriBlast
Commercial graphical software for Blast searches.
http://www.korilog.com/products/improving-NCBI-BLAST.php

limmaGUI
A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
http://bioinf.wehi.edu.au/limmaGUI/index.html

MaGe (Magnifying Genomes) - Microbial genome Annotation System
The MaGe system offers a set of graphical interfaces which allow biologist to perform relevant expert annotation of microbial genomes.
http://www.genoscope.cns.fr/agc/mage/

Mauve
Free software for constructing global alignments of multiple rearranged genomes. The visualization environment displays sequence similarity profiles and annotated sequence features.
http://gel.ahabs.wisc.edu/mauve/

MedScan
Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.
http://www.ariadnegenomics.com/products/medscan.html

MELTING
Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions.
http://www.ebi.ac.uk/~lenov/meltinghome.html

Meta-MEME
Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
http://metameme.sdsc.edu/

MIRA
A sequence assembly suite with SNP detection for "hard" projects.
http://chevreux.org/projects_mira.html

Nano+Bio-Centre
Offers a range of free software tools for annotating an entire genome, assembling sequences, gap closing and analysis of microarrays.
http://nbc3.biologie.uni-kl.de

NCBI BLAST
BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.
http://www.ncbi.nlm.nih.gov/BLAST/

pDRAW32
Freeware DNA cloning, analysis and visualization software.
http://www.acaclone.com

Phrap/Consed
DNA sequence assembler and finishing tools from the UW Genome Center.
http://www.phrap.org/

PHRED
A widely-used program for base calling DNA sequencing trace files. Source code available and free for non-commecial users.
http://www.genome.washington.edu/UWGC/analysistools/Phred.cfm

PhyloSort
A Java tool to sort phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
http://phylosort.sourceforge.net/

Premier Biosoft International
Developers of software for real time PCR primer design, TaqMan, molecular beacons, SYBR green, FRET, DNA microarray analysis, restriction cloning, plasmid maps, gateway cloning, protein interaction network and functional genomics.
http://www.premierbiosoft.com/

RGBG Analyzer
Commercial software to analyses the red, green, blue, and gray color values of user-selected areas of images in gif, tiff, bmp, jpeg format. Windows 2000 and XP.
http://www.immunokin.com

Seqtools
Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
http://www.seqtools.dk

Sequence Analysis
A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.
http://www.informagen.com/SA/

SeWeR
An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.
http://bioinformatics.org/sewer/

Sfold
Predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids. The web server version is free for academic use.
http://sfold.wadsworth.org/index.pl

Sockeye
3D visualisation platform for Comparative Genomics visualisation.
http://www.bcgsc.ca/gc/bomge/sockeye/

STRAP
Software supports the analysis of hundreds of proteins and integrates aa sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence, and residue annotation.
http://www.charite.de/bioinf/strap

Tandem Repeats Finder
Locates and displays tandem repeats in DNA sequences.
http://tandem.bu.edu/trf/trf.html

WU-BLAST
The Washington University improved version of BLAST. Free for academic users.
http://blast.wustl.edu/

XDigitize
A Linux/Unix visualization software system for evaluation of hybridisation experiments.
http://www.molgen.mpg.de/~xdigitise/